An ''urgent'' ministerial briefing note to the former special minister of state Eric Abetz warned that as far back as 2002 something was amiss with Peter Slipper's family travel expenses.
The note, obtained by The Sun-Herald under freedom-of-information laws, reveals Mr Abetz and other ministers were advised Mr Slipper had been spoken to ''on various occasions'' about his family travel entitlements, yet continued making expense claims that broke the rules.
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Further questions regarding Peter Slipper's travel expenses come to light.
Other documents obtained under FOI reveal the Howard government at the time prepared a brief titled ''hot issues'' just in case the matter was raised in an estimates hearing.
The suggested response was to say Mr Slipper had repaid the $5079.40 owing to the Commonwealth but in the background notes, headlined ''not for release'', it said ''Mr Slipper was critical of departmental processes in identifying apparent travel outside of entitlement.
Mr Slipper stood aside as Speaker of the House of Representatives two weeks after a staff member, James Ashby, filed a complaint in the Federal Court of sexual harassment, which included details of lewd text messages and allegations Mr Slipper had handed over signed Cabcharge dockets with blank amounts.
Mr Slipper has since released copies of the dockets claiming they are in his own handwriting and exonerate him. He has maintained that his travel expenditure is in order and within entitlement.
A string of emails and letters obtained under FOI between Mr Slipper and the Department of Finance shows he had run into trouble in 2002 claiming numerous trips in 2002 for his former wife, Lyn Slipper, and their children, Nicholas and Alexandra.
The department explained that a condition of family travel was that the person travelling must accompany or join the member. ''It has been established that this did not occur,'' said the department on eight occasions. The allowed interstate trip count had been exceeded.
The documents show that in the eight months between July 2002 and February 2003, Mr Slipper took flights worth $39,818 from far-flung places including Horn, Saibai and Boigu islands in the Torres Straits to Cairns, Alice Springs, Whyalla, Mount Gambier as well as Brisbane, Canberra, Sydney, Melbourne and Perth.
The Coalition was criticised for preselecting Mr Slipper on many occasions, despite the continuing questions about his drinking, his abuse of parliamentary entitlements and his relationship with aides. The Queensland Liberal party factional boss Santo Santoro ensured Mr Slipper was routinely preselected for his Sunshine Coast seat.
Former Howard government advisers and senior Liberal Party figures have told The Sun-Herald Mr Santoro's factional support for Mr Slipper protected him from being disendorsed.
''There was definitely a concern [about Mr Slipper] but he was entrenched,'' a former senior adviser in Mr Howard's prime ministerial office said. ''If you'd been able to move him on, you would [have], but you weren't able to. He had the numbers.''
A senior figure within the Queensland party concurred: ''He was very much a protected species … [Mr Santoro's faction] would use their influence to look after him. They did that for their own self-interest. It was a symbiotic relationship with Santo.''
Sources said Mr Slipper would marshal members of his electorate to back candidates favoured by Mr Santoro for party positions and preselections. John Howard attempted to rein in Mr Slipper's behaviour by appointing him his personal parliamentary secretary in March 2002. ''Howard wanted to keep a close eye on him,'' another former senior adviser to the Howard government said.
But the plan did not work, and rumblings about Mr Slipper's conduct continued. It is now alleged that in mid-2003, Mr Howard's adviser Tony Nutt was told a video existed showing Mr Slipper lying on a bed hugging a male aide ''in an intimate fashion''.
In October 2003, Mr Howard sacked Mr Slipper. ''He was such a problem they couldn't hide him in plain sight,'' the former adviser said. ''Peter never forgave Howard for sacking him.''
Mr Slipper's political colleagues pinpointed the end of his first marriage, a couple of years earlier, as a turning point in his fortunes.
Mr Slipper was married to Lyn Hooper, the daughter of a minister in the Joh Bjelke-Petersen government, for 15 years. The first Mrs Slipper was widely considered to be a smarter political operator than her husband. ''She was an ideal politician's wife,'' a Queensland Liberal Party figure who knew the Slippers said.